Covers: Chapter 15 - Unit tests

Unit Testing

Framework choice

  • Bioconductor slightly prefers testthat. RUnit and tinytest are also accepted.
  • testthat: active development, rich assertions, integrates with devtools, informative failures.
  • tinytest: lightweight, zero dependencies.
  • RUnit: long Bioconductor history but unmaintained since ~2010.
  • Declare the framework in DESCRIPTION Suggests: (e.g. Suggests: testthat, or Suggests: RUnit, BiocGenerics, or Suggests: tinytest).

Directory structure and naming

  • testthat: tests in tests/testthat/, files start with test. Set up with usethis::use_testthat().
  • RUnit: tests in inst/unitTests/, files match test_*.R (e.g. test_divideBy.R). Add tests/runTests.R containing: BiocGenerics:::testPackage("MyPackage").
  • tinytest: tests in inst/tinytest/. Add tests/tinytest.R: if (requireNamespace("tinytest", quietly=TRUE)) tinytest::test_package("PACKAGE").

What to test

  • Test functions, methods, and classes with known inputs and expected outputs.
  • Test edge cases and error conditions, not only the happy path.
  • No hard minimum coverage percentage is mandated, but higher coverage is expected and reduces bug risk.

Coverage measurement

  • Use the covr package: covr::package_coverage().

Running tests

  • Full check (runs all tests): R CMD check MyPackage.
  • During development: devtools::test() (reloads code and reruns).
  • Manual: source the package and test files, then call the test function.

Long-running tests

  • Tests in tests/ must finish within 40 minutes as part of R CMD check.
  • Tests too slow for that belong in a longtests/ directory at the top level of the package, alongside tests/, with a .BBSoptions file at the top level containing RunLongTests: TRUE. They are given up to 6 hours.
  • Long tests run weekly (Saturdays) on their own builders, on both devel and release. Their failures do not block propagation after a version bump; only the nightly tests/ results do.
  • longtests/ is structured like tests/ and typically runs unit tests, but no framework is mandated.
  • Reach out to the bioc-devel mailing list before adding long tests, so their use is justified and they do not slow the builds.
  • This is the alternative to deleting coverage or skipping it on the Bioconductor builders: skipping (skip_on_bioc(), and similar guards) means the nightly builds never exercise that code, so regressions in it go unnoticed.
  • Long tests do not apply to vignettes. A vignette is evaluated during the build, so a chunk that is slow needs a smaller example, precomputed results shipped with the package, or caching – not longtests/ and not eval=FALSE.

Source: Unit tests , Long tests , Advanced build options Fetched 2026-08-14 from contributions.bioconductor.org (Bioconductor devel guide). “Long-running tests” was verified 2026-09-26 against the Long tests page and tests.html 15.5, which links to it; the mechanism is also summarised in Appendix B of ../appendices.md.

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